Conceptual Biology and Medicine
The goal of our interdisciplinary team is to explore the conceptual and foundational bases of today’s biology and medicine. We reach this aim through what we call ‘Philosophy in biology’, an innovative way to combine the contributions of philosophy of biology, experimental biology, computational biology, and medical biology. We are focused first and
foremost on the immune system, cancer, aging, and the microbiome, although we also work on conceptual issues related to evolutionary biology, ecology, developmental biology, physiology, and the medical sciences in general. Our goal is to intervene in decisions that precede experiments, in order to maximize the chances of results.
- Head : Thomas Pradeu & Maël Lemoine
- Univ. Bordeaux, CNRS UMR5164
Discover
Our research activity is divided into five axes. These axes do not represent disjoint subgroups, but rather thematic foci to which all team members may contribute at different times and to varying degrees. The first axis (“Conceptual Immunology”) investigates core concepts of immunology and puts forward an alternative view of the immune system beyond the idea of host defense. The second axis (“Cancer”) is dedicated to a deeper understanding of cancer that takes into account the role of the microenvironment, the evolutionary context, and the possible links to processes involved in aging. The third axis (“How aging causes age-related diseases”) addresses major conceptual problems concerning the mechanisms of aging and their relationship to age-related diseases. The fourth axis ( “Computational methods in biology and medicine”) aims at developing a conceptual framework to understand and facilitate the integration of computational methods in the biomedical sciences, notably in the context of immunology. Finally, the fifth axis (“Microbiome: symbiosis, immunity, and cancer”) proposes new theoretical tools to study the symbiotic relationships between organisms and their microbial communities.
Our team is a pillar of the Institute for Philosophy in Biology and Medicine (PhilInBioMed), an interdisciplinary institute located at the University of Bordeaux, France, and a national and international network of interdisciplinary institutes. PhilInBioMed aims at promoting philosophy in the biological and medical sciences.
Conceptual immunology
Exploring central concepts and theories in immunology and showing that they make difference in experimental and clinical practice.
Cancer
Developing new conceptualizations and new methods for investing cancer and determining the evolutionary landmarks of cancer.
How aging causes age-related diseases
Conceptual clarification of major problems in aging research, developing a multilayer evolutionary view of aging and determining the foundations of Geroscience
Computational methods in biology and medicine
Understanding and addressing the challenges of integrating computational methods into different areas of biology and medicine.
Microbiome: symbiosis, immunity, and cancer
Exploring how the microbiome influences health and disease, especially via its interactions with the immune system, and particularly in the case of cancer.
Publications
- Bazin T, Chiu L, Pradeu T (2022) Host-Microbiota Co-immunity: An Intimate Relationship That Goes Beyond Protection. Philosophy, Theory, and Practice in Biology 14.
- Sholl, J (2022), Everything in Moderation or Moderating Everything? Nutrient balancing in the context of evolution and cancer metabolism. Biology & Philosophy 37(14).
- Torri A, Jaeger J, Pradeu T, Saleh M-C (2022), The origin of RNA interference: Adaptive or neutral evolution? PLOS Biology 20(6), e3001715.
- Lemoine, M. (2022), La médecine personnalisée annonce-t-elle la fin du diagnostic ? In Arminjon et al. (eds.), Le normal et le pathologique : des catégories périmées ? Paris: Matériologiques, 77‑89.
- Guerville F, Bourdel-Marchasson I, Déchanet-Merville J, Pellegrin I, Soubeyran P, Appay V, Lemoine M (2022), Does Inflammation Contribute to Cancer Incidence and Mortality during Aging? A Conceptual Review. Cancers 14(7), 1622.
- Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R (2022), Cancer’s second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process. BioEssays 44(5), e2100252.
- Laurent P, Lapoirie J, Leleu D, Levionnois E, Grenier C, Jurado-Mestre B, Lazaro E, Duffau P, Richez C, Seneschal J, Pellegrin J-L, Constans J, Schaeverbeke T, Douchet I, Duluc D, Pradeu T, Chizzolini C, Blanco P, Truchetet M-E, Contin-Bordes, C. (2022), Interleukin-1-β-Activated Microvascular Endothelial Cells Promote DC-SIGN+ Alternative Macrophages Associated with Skin Fibrosis in Systemic Sclerosis. Arthritis & Rheumatology 74(6), 1013-1026.
- Soutschek M, Gross F, Schratt, G, Germain P-L (2022), ScanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction, Bioinformatics 38(9), 2466–2473.
- Sholl J, Sepich-Poore GD, Knight R, Pradeu T (2022), Redrawing therapeutic boundaries: microbiota and cancer. Trends in Cancer 8(2), 87-97.
- Tabb, K & Lemoine M (2022), The prospects of precision psychiatry. Theoretical Medicine and Bioethics 42, 193–210.
- Alexa A, Sok P, Gross F et al. (2022) A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host. Nature Communications 13, 472.
- Kaminski H, Lemoine M, Pradeu T (2021), Immunological exhaustion: How to make a disparate concept operational? PLOS Pathogens 17, e1009892.
- Laurent P, Allard B, Manicki P, Jolivel V, Levionnois E, Jeljeli M, Henrot P, Izotte J, Leleu D, Groppi A, Seneschal J, Constans J, Chizzolini C, Richez C, Duffau P, Lazaro E, Forcade E, Schaeverbeke T, Pradeu T, Batteux F, Blanco P, Contin-Bordes C, Truchetet ME (2021), TGFβ promotes low IL10-producing ILC2 with profibrotic ability involved in skin fibrosis in systemic sclerosis, Annals of the Rheumatic Diseases 80:1594-1603.
- Harly, C, Joyce, SP, Domblides, C, Bachelet, T, Pitard, V, Mannat, C, Pappalardo, A, Couzi, L, Netzer, S, Massara, L, Obre, E, Hawchar, O, Lartigue, L, Claverol, S, Cano, C, Moreau, J-F, Mahouche, I, Soubeyran, I, Rossignol, R, Viollet, B, Willcox, CR, Mohammed, F, Willcox, BE, Faustin, B and Déchanet-Merville, J (2021), Human gd Cell Sensing of AMPK-Dependent Metabolic Tumor Reprogramming through TCR Recognition of EphA2. Science Immunology, 6, 61.
- Loison L, Pradeu T (eds. 2021) La Biologie au défi de l’histoire : Mélanges offerts à Michel Morange. Paris, Éditions Matériologiques.
- Bienvenu T, Dejean C, Jercog D, Aouizerate B, Lemoine M, Herry C (2021) The advent of fear conditioning as an animal model of post-traumatic stress disorder: Learning from the past to shape the future of PTSD research.
- Abrous DN, Koehl M, & Lemoine M (2021) A Baldwin interpretation of adult hippocampal neurogenesis: from functional relevance to physiopathology. Mol Psychiatry.
- Pradeu T, Lemoine M, Khelfaoui M, Gingras Y (2021) Philosophy in Science: Can philosophers of science permeate through science and produce scientific knowledge? The British Journal for Philosophy of Science.
- Sholl J, Mailing LJ, Wood TR (2021), Reframing nutritional microbiota studies to reflect an inherent metabolic flexibility of the human gut: a narrative review focusing on high-fat diets. mBio.
- Sholl J (2021), Can aging research generate a theory of health?, History and Philosophy of the Life Sciences.
- Sholl J, Okholm S (2021), Taking a Naturalistic Turn in the Health and Disease Debate. Teorema.
- Khelfaoui M, Gingras Y, Lemoine L, Pradeu T (2021), The visibility of philosophy of science in the sciences, 1980-2018, Synthese. (PDF of final draft).
- Greslehner G (2021), The vaccinologist’s “dirty little secret”: a better understanding of structure-function relationships of viral immunogens might advance rational HIV vaccine design. Archives of Virology. (Open access).
- Gayon J & Pradeu T (eds., 2021), Textes Clés en Philosophie de la Biologie. Tome 1 : Explication biologique, hérédité, développement. Tome 2 : Évolution, environnement, diversité biologique. Paris, Vrin.
- Lemoine M (2021) Is the Dysfunction Component of the “Harmful Dysfunction Analysis” Stipulative? In: L. Faucher and Forest D (eds) Defining mental disorder: Jerome Wakefield and his critics. The MIT Press, Cambridge, Massachusetts, pp 199–212 (open access).
- Nardini C & Gross F (2021), Grassroots Modeling during the Covid-19 Pandemic, ARGUMENTA 7, 161-178.
- Lemoine M (2021), The Evolution of the Hallmarks of Aging, Frontiers in Genetics 12, 693071.
- Lemoine M. (2020), Defining aging. Biology & Philosophy 35: 46 (preprint).
- Paludan S.R., Pradeu T., Masters S., Mogensen T. (2020), Constitutive immune mechanisms: mediators of host defence and immune regulation. Nature Reviews Immunology. (Open access).
- Greslehner G. (2020), Not by structures alone: Can the immune system recognize microbial functions? Studies in History and Philosophy of Biological and Biomedical Sciences. (Open access).
- Ronai I., Greslehner G., et al. (2020), Microbiota, symbiosis and individuality Summer School Meeting Report, Microbiome 8, 117 (Report on ERC IDEM summer school in Biarritz). (Open access)
- Greslehner G. (2020), Microbiome Structure and Function: A New Framework for Interpreting Data. BioEssays.
- Richez C., Lazaro E., Lemoine M.,Truchetet ME., Schaeverbeke T. (2020), Implications of COVID-19 for the management of patients with inflammatory rheumatic diseases. Joint Bone Spine 87, 187–189.
- Chiu L. & Gilbert S. (2020), Niche construction and the transition to herbivory: Phenotype switching and the organization of new nutritional modes. In Levine et al. (eds.), Phenotypic Switching: Implications in Biology and Medicine. London, Academic Press, 459-482.
- Belzung, C., Billette de Villemeur, E. and Lemoine, M. (2020): Mechanistic vs Statistical Extrapolation in Preclinical Research in Psychiatry: Challenging the Received View, in A. LaCaze and B. Osimani (eds), Uncertainty in Pharmacology, Vol. 338 Cham: Springer International Publishing, pp. 79–100 (The chapter as open access).
- Greslehner G. and Lemoine M. (2020), A dual decomposition strategy of both microbial and phenotypic components for a better understanding of causal claims. Biology & Philosophy 35:1.
- Guay A. & Pradeu T. (2020), Right out of the box: How to situate metaphysics of science in relation to other metaphysical approaches. Synthese, 197, 1847–1866. In special issue on “New Metaphysics of Science” edited by Max Kistler. (PDF of final draft).
- Pradeu T. (2019), Philosophy of Immunology. Cambridge University Press, Elements in Philosophy of Biology Series (Open Access).
- Rondeau E., Larmonier N., Pradeu T., Bikfalvi A. (co-senior authors) (2019) Philosophy of Biology: Characterizing causality in cancer. eLife 8:e53755. (Open Access).
- Laplane L., Duluc D., Bikfalvi A, Larmonier N., and Pradeu T. (2019), Beyond the tumour microenvironment. International Journal of Cancer 145(10), 2611-2618. (Open Access).
- Pradeu T. (2019), Philosophy of Biology: Immunology and individuality, eLIFE 8:e47384. (Open Access).
- Laplane L., Mantovani P., Adolphs R., Chang H., Mantovani A., McFall-Ngai M., Rovelli C., Sober E., and Pradeu T. (2019), Why science needs philosophy. Proceedings of the National Academy of the Sciences USA (PNAS) 116 (10) 3948-3952. (Open access).
- Bich L., Pradeu T., and Moreau J-F. (2019), Understanding Multicellularity: The Functional Organization of the Intercellular Space. Frontiers in Physiology 10:1170 (Open Access).
- Pradeu T. (2019), Philosophy of CRISPR-Cas. Biology & Philosophy 34(16). (Open access). (PDF of final draft).
- Pradeu T & Moreau J-F. (2019), CRISPR-Cas immunity: Beyond nonself and defence. Biology & Philosophy 34(6). (PDF of final draft).
- Laplane L., Duluc D., Larmonier N., Pradeu T. & Bikfalvi A. [co-senior authors] (2018), The Multiple Layers of the Tumor Environment. Trends in Cancer 4, 802–809. (PDF of final draft).
- Lemoine M. & Pradeu T. (2018), Dissecting the meanings of ‘Physiology’ to assess the vitality of the discipline. Physiology 33(4), 236-245. (Open Access PDF) (PDF of final draft).
- Pradeu T. & Du Pasquier L. (2018), Immunological memory: What’s in a name? Immunological Reviews 283(1) (Special Issue: Immunologic Memory), 7-20. (PDF of final draft).
- Giroux É., Lemoine M. (2018), Philosophy of Medicine, chapter in The Philosophy of Science: A Companion, Oxford University Press.
- Pradeu, T. (2018), Philosophy of Biology, chapter in The Philosophy of Science: A Companion, Oxford University Press.
- O’Malley M.A. (2018), The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology, J Hist Biol. 2018 Jun;51(2):319-354.
- Truchetet M-E. & Pradeu T. (2018), Re-thinking our understanding of immunity: Robustness in the tissue reconstruction system. Seminars in Immunology 36, 45-55. (PDF of final draft).
- Eberl G. & Pradeu T. (2018), Towards a General Theory of Immunity? Trends in Immunology 39 (4), 261-263.
- Lemoine M. (2018), On the neurobiological redefinition of psychiatric symptoms: elimination, reduction, or what?, Synthese, online (doi: 10.1007/s11229-016-1270-2).
- Pradeu T. (2018), Genidentity and Biological Processes, in Nicholson, D. J. & Dupré, J. (eds.). Error! Hyperlink reference not valid.. Oxford: Oxford University Press.
- O’Malley M. A., Skillings D. J. (2018), Methodological strategies in microbiome research and their explanatory implications, Perspectives on Science 26(2): 239–265.
- Lemoine M. (2017), Neither from words, nor from vision: understanding p-medicine from innovative treatments, Lato sensu 4(2). (Open Access).
- Chiu L., Bazin T. (co-first authors), Truchetet M-E., Schaeverbeke T., Delhaes L. & Pradeu T. (2017), Protective Microbiota: From Localized to Long-Reaching Co-Immunity. Frontiers in Immunology, December 2017, Volume 8, Article 1678. (Open Access).
- Hooks K.B. & O’Malley M. (2017) Dysbiosis and Its Discontents. mBio 8:e01492-17. (Open Access).
- Ferner A. & Pradeu T. (eds., (2017) Special issue on “Ontologies of Living Beings“, Philosophy, Theory, and Practice in Biology, Volume 9. Editorial by A. Ferner & T. Pradeu. Contributors to this special issue: Stéphane Chauvier, Melinda Fagan, Fridolin Gross & Sara Green, Catherine Kendig & Todd Eckdahl, Rory Madden, John Perry, and Christopher Shields. (Open Access).
- Laurent P., Jolivel V., Manicki P., Chiu L., Cotin-Bordes C., Truchetet M-E. & Pradeu. T. (co-senior authors) (2017), Immune-Mediated Repair: A Matter of Plasticity. Frontiers in Immunology, April 2017, Volume 8, Article 454. (Open Access).
- Pradeu T. (2017), Thirty years of Biology & Philosophy: Philosophy of which biology? Biology & Philosophy 32(2), 149–167. (PDF of final draft).
- Lemoine M. (2017), Animal Extrapolation in Preclinical Studies. An analysis of the tragic case of TGN1412, Studies in the History and Philosophy of Biological and Biomedical Science, 61, 35-45.
- Lemoine M. (2017), Introduction à la philosophie des sciences médicales, Hermann, Paris.
- Moreau J-F., Pradeu T., Grignolio A., Nardini C., Castiglione F., Tieri P., Capri M., Salvioli S., Taupin J-L., Garagnani P. & Franceschi C. (2017), The re-emerging role of ECM crosslinking in T cell mobility as a hallmark of immunosenescence. Ageing Research Reviews 35, 322–335. (Open Access).
- Furman D., Chang J., Lartigue L., Bolen C.R., Haddad F., Gaudilliere B., Ganio E.A., Fragiadakis G.K., Spitzer M.H., Douchet I., Daburon S., Moreau J.F., Nolan G.P., Blanco P., Déchanet-Merville J., Dekker C.L., Jojic V., Kuo C.J., Davis M.M., & Faustin B. (2017), Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states. Nature Medicine 23, 174-184.
- Marlin R, Pappalardo A, Kaminski H, Willcox CR, Pitard V, Netzer S, Khairallah C, Lomenech AM, Harly C, Bonneville M, Moreau JF, Scotet E, Willcox BE, Faustin B and Dechanet-Merville J. (2017), Sensing of cell stress by human γδ TCR-dependent recognition of Annexin A2. Proceedings of the National Academy of Sciences (USA) 114, 3163-3168.
- Lemoine MP. (2016) Extrapolation from animal model of depressive disorders: what’s lost in translation?, in S. Demazeux & J. Wakefield (eds), Sadness or Depression? International Perspectives on the Depression Epidemic and Its Meaning, Springer, 157-172.
- Lemoine M. & Giroux E. (2016) Is Boorse’s Biostatistical Theory of Health naturalistic?, in E. Giroux (ed), Naturalism in philosophy of health: challenges, issues and implications, Springer, 19-38.
- Lemoine M. (2016) « Molecular complexity: Why has psychiatry not been revolutionized by genomics (yet)? », in G. Boniolo & M. Nathan (eds.), Foundational Issues in Molecular Medicine, Routledge, London, 81-99.
- Lemoine M. (2016) « Explanation in Medicine », in M. Solomon, H. Kincaid and J. Simon (eds.), The Routledge Companion to Philosophy of Medicine, Routledge, New York, 296-310.
- Pradeu T., Laplane L., Prévot K., Hoquet T., Reynaud V., Fusco G., Minelli A., Orgogozo V., Vervoort M. (2016), Defining “Development”, Current Topics in Developmental Biology, Volume 117, Pages 171-183.
- Pradeu T. (2016), Editorial introduction: The many faces of biological individuality. Special issue on biological individuality, T. Pradeu, ed., Biology & Philosophy 31(6), 761-773.
- Pradeu T. (2016), Organisms or biological individuals? Combining physiological and evolutionary individuality. Biology and Philosophy 31(6), 797–817.
- Chiu L. & Eberl G. (2016), Microorganisms as scaffolds of host individuality: an eco-immunity account of the holobiont. Biology and Philosophy 31(6), 819-837.
- Skillings D. (2016), Holobionts and the ecology of organisms: Multi-species communities or integrated individuals? Biology & Philosophy 31(6), 875-892.
- Pradeu T. & Vivier E. (2016), The Discontinuity Theory of Immunity, Science Immunology Vol. 1, Issue 1, pp. aag0479.
- Bich, L. and Moreno, A. (2016). The role of regulation in the origin and synthetic modelling of minimal cognition. BioSystems, 148, 12-21.
- Bich, L., Mossio, M., Ruiz-Mirazo, K. and Moreno, A. (2016). Biological regulation: controlling the system from within. Biology & Philosophy, 31(2), 237-265.
- Guay A. & Pradeu T. (eds.) (2016) Individuals Across the Sciences. New York: Oxford University Press.
- Pradeu T. (2016), Mutualistic viruses and the heteronomy of life, Studies in History and Philosophy of Biological and Biomedical Sciences 59, 80-88.
- Pradeu T., Kostyrka G., and Dupré J (2016), Understanding viruses: Philosophical investigations, Studies in History and Philosophy of Biological and Biomedical Sciences 59, 57-63.
- O’Malley MA (2016). The ecological virus. Studies in History and Philosophy of Biological and Biomedical Sciences 59: 71–79.
- O’Malley MA (2016), Microbiology, philosophy and education, FEMS Microbiology Letters, Volume 363, Issue 17.
- O’Malley MA, Wideman JG, Ruiz-Trillo I. (2016), Losing complexity: The role of simplification in macroevolution. Trends in Ecology and Evolution 31: 608–621.
- O’Malley MA (2016), Reproduction expanded: Multigenerational and multilineal units of evolution, Philosophy of Science.
- Pradeu, T., (2016), Toolbox murders: putting genes in their epigenetic and ecological contexts. Biol Philos 31, 125–142.
- Lemoine M. (2013), Defining disease beyond conceptual analysis: an analysis of conceptual analysis in philosophy of medicine. Theoretical Medicine and Bioethics 34(4), 309-325.
- Pradeu T., Jaeger S., Vivier E. (2013), The Speed of Change: Towards a Discontinuity Theory of Immunity? Nature Reviews Immunology 13, 764–769.
- Pradeu T. (2012), The Limits of the Self: Immunology and Biological Identity. New York: Oxford University Press (2015 Lakatos Award).
- Pradeu T., Cooper E.L. (2012), The Danger Theory: Twenty Years Later. Frontiers in Immunology 3: 287.
- Belzung C., Lemoine M. (2011), Criteria of validity for animal models of psychiatric disorders: focus on anxiety disorders and depression. Biology of Mood & Anxiety Disorders 1: 9 (Open Access).
- Pradeu T. (2010), What is an organism? An immunological answer. History and Philosophy of the Life Sciences 32: 247-268.
- Pradeu T. & Carosella E.D. (2006), On the definition of a criterion of immunogenicity. Proceedings of the National Academy of the Sciences USA (PNAS), 103(47): 17858-61.
- Carosella E.D., Pradeu T. (2006), Transplantation and Identity: A Dangerous Split. The Lancet 368(9531): 183-184.
- Moreau J-F. et al. (1988), Leukaemia inhibitory factor is identical to the myeloid growth factor human interleukin for DA cells. Nature 336, 690-692.
Past members
- Imane BARBARA (Now Project Manager in Strasbourg)
- Leonardo BICH (Now Ramon y Cajal senior researcher at the University of the Basque Country, Spain)
- Wiebke BRETTING (Now Project Manager in a Bordeaux hospital-hosted project)
- Lynn CHIU (Now Media and Communications Officer, Konrad Lorenz Institute for Evolution and Cognition Research (KLI) & Extended Evolutionary Synthesis research project, University of St. Andrews)
- Nicolas DUSSECH (Intern in Biology)
- Gregor GRESLEHNER (Now Lecturer at the University of Vienna)
- Katarzyna HOOKS (Now Postdoctoral researcher)
- Valérie JOLIVEL (Now Associate Professor of Biology in Strasbourg)
- Paôline LAURENT (Now Postdoctoral researcher in New York)
- Maureen O’MALLEY (Now Senior researcher at the University of Sydney)
- Elena RONDEAU (PhD student w/ T. Pradeu, 2017-2021, now Lecturer at the Ecole Normale Superieure in Lyon)
- Derek SKILLINGS (Now Assistant Professor of Philosophy at UNC Greensboro, USA)
Recent visitors
- Mina BISSELL, Professor of Biology, University of Berkeley, USA.
- Peter GODFREY-SMITH, Professor in Philosophy of Science, University of Sydney, Australia
- Deborah GORDON, Professor of Biology, Stanford University, USA
- Paul GRIFFITHS, Professor in Philosophy of Science, University of Sydney, Australia
- Fridolin GROSS, Postdoctoral researcher, University of Kassel, Germany
- Valerie HARDCASTLE, Professor of Philosophy and Psychology, University of Cincinnati, USA
- Alberto MANTOVANI, Professor of Medicine, Humanitas, Italy.
- Jacob STEGENGA, Lecturer in Philosophy of Science, University of Cambridge, UK
- Adrian STENCEL, PhD Student Jagiellonian University, Krakow, Poland
- Martin ZACH (visiting PhD student from Oct.-Dec. 2019 and will be an EPSA Fellow in our team in the near future)
- Javier SUAREZ, Postdoctoral Researcher, University of Bielefeld, Germany
Funding
